search

GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
374 stars 133 forks source link

Motif Analysis #460

Closed e-arslan closed 3 years ago

e-arslan commented 3 years ago

What is the reason to get a slightly different TF ranking on motif analysis when I run the code at different times?

Here are the steps before TF ranking at different runs:

  1. loadArchRProject
  2. addGroupCoverages
  3. addReproduciblePeakSet
  4. addPeakMatrix
  5. addMotifAnnotations
  6. getMarkerFeatures
  7. peakAnnoEnrichment
rcorces commented 3 years ago

I believe what you are seeing is a result of randomization during the addGroupCoverages() function. This function creates pseudo-bulked replicates based on the parameters that you designate and there is randomization involved in how groups of cells are selected. The results should be very similar albeit not identical though.

Please close this issue if this has answered your question.

e-arslan commented 3 years ago

thanks for the answer.